Variant report

Variant	rs12975396
Chromosome Location	chr19:41173372-41173373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41167496..41181822-chr19:41192475..41200102,20	MCF-7	breast:
2	chr19:41167833..41170600-chr19:41173317..41176394,3	MCF-7	breast:
3	chr19:41167372..41175149-chr19:41187518..41198541,22	K562	blood:
4	chr19:41166318..41173902-chr19:41219711..41223853,11	K562	blood:
5	chr19:41171985..41176323-chr19:41183438..41185742,3	MCF-7	breast:
6	chr19:41171413..41174088-chr19:41312213..41313806,2	MCF-7	breast:
7	chr19:41170975..41174075-chr19:41207359..41209061,3	K562	blood:
8	chr19:41172247..41174335-chr19:41222503..41224165,2	MCF-7	breast:
9	chr19:41171166..41174388-chr19:41302403..41306286,4	K562	blood:
10	chr19:41171645..41173903-chr19:41256454..41259241,2	K562	blood:
11	chr19:41165880..41175149-chr19:41192911..41198858,17	K562	blood:
12	chr19:41171300..41174250-chr19:41255896..41258297,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188493	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11665867	0.88[LWK][hapmap]
rs11668501	0.89[ASW][hapmap];0.96[LWK][hapmap]
rs11673492	0.89[ASW][hapmap];1.00[CHB][hapmap]
rs11881578	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459415	0.83[EUR][1000 genomes]
rs12984927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343945	0.98[EUR][1000 genomes]
rs34433534	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34547501	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34605579	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34652347	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34689418	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35172225	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35625703	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35687546	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35735265	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58429803	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247247	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7253502	0.89[ASW][hapmap];0.88[LWK][hapmap]
rs7508466	0.97[EUR][1000 genomes]
rs8104739	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105009	0.88[ASW][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
9	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12975396	LMTK3	cis	cerebellum	SCAN
rs12975396	STRN4	cis	parietal	SCAN
rs12975396	EMP3	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41169600-41173800	Weak transcription	Small Intestine	intestine
2	chr19:41169600-41174000	Weak transcription	Primary T cells from cord blood	blood
3	chr19:41169800-41173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:41169800-41173600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr19:41169800-41174400	Weak transcription	Brain Angular Gyrus	brain
6	chr19:41169800-41175000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:41169800-41175000	Weak transcription	Brain Substantia Nigra	brain
8	chr19:41169800-41175000	Weak transcription	Fetal Heart	heart
9	chr19:41169800-41175000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:41169800-41184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:41169800-41195400	Weak transcription	Psoas Muscle	Psoas
12	chr19:41170000-41173400	Weak transcription	Pancreas	Pancrea
13	chr19:41170000-41173600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:41170000-41173600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:41170000-41173800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:41170000-41173800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:41170000-41174000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:41170000-41174000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:41170000-41174000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:41170000-41174000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:41170000-41174000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:41170000-41174000	Weak transcription	Fetal Lung	lung
23	chr19:41170000-41174000	Weak transcription	Dnd41	blood
24	chr19:41170000-41174000	Weak transcription	HSMMtube	muscle
25	chr19:41170000-41174200	Weak transcription	Fetal Kidney	kidney
26	chr19:41170000-41174600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:41170000-41174600	Weak transcription	Primary B cells from cord blood	blood
28	chr19:41170000-41174600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:41170000-41174600	Weak transcription	Fetal Thymus	thymus
30	chr19:41170000-41174800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:41170000-41175000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr19:41170000-41175000	Weak transcription	GM12878-XiMat	blood
33	chr19:41170000-41175200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:41170000-41175400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr19:41170000-41178400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:41170000-41180400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:41170000-41180400	Weak transcription	Right Atrium	heart
38	chr19:41170000-41180800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:41170200-41173800	Weak transcription	Left Ventricle	heart
40	chr19:41170200-41174200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:41170200-41174200	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:41170200-41174600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:41170200-41174600	Weak transcription	Fetal Brain Male	brain
44	chr19:41170200-41174600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:41170200-41174800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:41170200-41174800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:41170200-41175000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:41171000-41173600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:41171000-41173600	Weak transcription	Placenta	Placenta
50	chr19:41171000-41174400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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